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pggb
the pangenome graph builderodgi
Optimized Dynamic Genome/Graph Implementation: understanding pangenome graphssmoothxg
linearize and simplify variation graphs using blocked partial order alignmentimpg
implicit pangenome graphmaffer
extract MSAs from genome variation graphsPanSN-spec
Pangenome Sequence Naming: a backwards-compatible hack to simplify the identification of samples and haplotypes in pangenomesvcfbub
use variant nesting information to flter overlapping sites from vg deconstruct outputpgge
the pangenome graph evaluatorpgvf-spec
Pangenome Graph Variation Format (PGVF)HPRCyear1v2genbank
building a human pangenome from the HPRCy1v2 genbank accessioned assembliespggb-workshop
tutorial on pggbspodgi
RDF and SPARQL ideas to build on top of [odgi](https://github.com/pangenome/odgi)pggb-paper
The PanGenome Graph Buildergfagino
your friendly pangenome graph genotyperpangenome.github.io
jbrowse-visualization
Workflow to visualize pggb graphs in jbrowseMemPanG23
Computational Pangenomics in Memphisgfa-wp
Convert GFA W-lines to P-linesresolve-nested-genotypes
chm13-grch38-liftover
liftover from the CHM13 T2T assembly to GRCh38 using wfmashlifetree
hard mode all genomes alignmentchromosome_communities
Recombination between heterologous human acrocentric chromosomesHPRCy1
pangenome build for HPRC year 1 samplesssfog
scale-space filtering on genome graphsrs-peanut
GAF alignment evaluation tool.mafchunk
split MAF blocks into smaller chunkssorting-paper
Path-Guided Stochastic Gradient Descent layout of pangenome graphsMHC
exploring the MHC in the HPRC year 1 samplesphage-evo-paper
Repository to store the analysis of the paper on phage evolution.seqwish-paper
Unbiased pangenome graphsgfalace
lace up GFA files using panSN path name sub-ranges to coordinate the lacingdomibubble
sketch of bubble detection via dominator treesprivacy-pangenomics
HumanPangenomeBYOD2024
Material for the Human Pangenome Bring Your Own Data (BYOD) analysis Workshop 2024, October 21-25 in Cape Town, South Africa.paf2dot
use gnuplot to generate a dotplot from sequence alignments in PAF formatodgi-paper
ODGI: understanding pangenome graphs (https://doi.org/10.1093/bioinformatics/btac308)odgi.github.io
ODGI suite documentation (Optimized Dynamic Genome/Graph Implementation)keane_mouse_pangenome
HPRCy1v2
pangenome build for human pangenome project year 1 genomes (version 2 assemblies)private-graphs-website
Privacy preserving graphs for pangenomicsflubble
finding single-entry single-exit bubbles in the flowgraphLove Open Source and this site? Check out how you can help us